Rev Language Reference
dnCTMC
Usage
dnCTMC(RateGenerator Q, Simplex rootFrequencies, Simplex siteMatrices, RealPos[] siteRates, Simplex siteRatesProbs, Natural nSites, String type)
Arguments
| Q : | RateGenerator (pass by const reference) |
| The global or site-mixture rate matrices. | |
| rootFrequencies : | Simplex (pass by const reference) |
| The root specific frequencies of the characters, if applicable. | |
| Default : NULL | |
| siteMatrices : | Simplex (pass by const reference) |
| Simplex of site matrix mixture probabilities. Treats Q as vector of site mixture categories instead of branch-specific matrices. | |
| Default : NULL | |
| siteRates : | RealPos[] (pass by const reference) |
| The rate categories for the sites. | |
| Default : [ ] | |
| siteRatesProbs : | Simplex (pass by const reference) |
| The probability weights of rate categories for the sites. | |
| Default : NULL | |
| nSites : | Natural (pass by value) |
| The number of sites, used for simulation. | |
| Default : 0 | |
| type : | String (pass by value) |
| The data type, used for simulation and initialization. | |
| Default : DNA | |
| Options : DNA|RNA|AA|Codon|PoMo|Protein|Standard|NaturalNumbers|Binary|Restriction |
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